I recognize, and fully understand, that this data maybe emotionally difficult to work. My intention is to make these lab relevant, allowing you to gather your own insights directly from new visualizations of the data. Please let me know if you would rather not work with the data.

Learning Objectives

Creating Country, State and County maps

The ideas for this course tutorial came from multiple examples contributed by Prof. Chris Sutherland and these tutorials

  1. Maps in R using maps by Eric Anderson
  2. geom_maps
  3. Drawing beautiful maps programmatically with R, sf and ggplot2

For our labs two types of approaches will be used to add data to maps. The first that we worked with last week is based on using the longitude and latitude information to add a point at a specific position on a map. The second is two add the information to shapes in a map based on the name of the shape (e.g. states). Although ggmaps is a wonderful tool for mapping using Google Maps and other resources, it is beyond what is needed for now.

As in the previous labs the sources of data are from Github repo for Novel Coronavirus (COVID-19) Cases that supports the dashboard.

For this lab it is important to note that the time series data does not currently have entries for US States. The daily reports include US State and more recently US country/administrative units. Is possible to concatenate the daily reports to create a time series for US States, but cognizant of changes in the formats of the daily reports.

Building maps

Here is a graph containing all the coordinate information. Note this is not summarized by country. Since there are now main points for US counties, there are many points in the US

Zoom in on US 48 states. To do this Alaska, Hawaii and US Territories are filtered. Some US State entries have a Lat and Long of zero, so these are filtered as well.

Here is a prettier version based on an example by Anisa Dhana

  • Note that in both examples the ggplot funtion borders is used to define the areas in the map

Mapping data to shapes

Using R color palattes

This is a bit of a digression back to Labs 3 and 4, but there are many R color palattes to choose from or you can create your own. In the above a simple gradient is used. The example from Anisa Dhana uses the viridis palatte which is designed to be perceived by viewers with common forms of colour blindness. Here is an example using a different color package - Wes Anderson. …and more Top R Color Palettes to Know for Great Data Visualization

A look now by the counties using the RColorBrewer

If we look at just Massachusetts

  • Note the cases on Nantucket and Dukes counties were reported as one value and not included on the graph. There is also an asssigned category that includes 303 Confirmed cases as of 3/31/2020.
## # A tibble: 14 x 2
##    Admin2              Confirmed
##    <chr>                   <dbl>
##  1 barnstable                283
##  2 berkshire                 213
##  3 bristol                   424
##  4 dukes and nantucket        12
##  5 essex                    1039
##  6 franklin                   85
##  7 hampden                   546
##  8 hampshire                 102
##  9 middlesex                1870
## 10 norfolk                   938
## 11 plymouth                  621
## 12 suffolk                  1896
## 13 unassigned                270
## 14 worcester                 667

Interactive graphs

In Lab 5 plotly was introduced. It is a great simple way to make interactive graphs with the maps

Exercises

  1. For the above graph “World COVID-19 Confirmed case” summarize the counts for each Country on the graph and update the graph to 9/26/2020. You may need to adjust the size of the points.

  2. Update Anisa Dhana’s graph layout of the US to 9/26/2020. You may need to adjust the size of the points.

  3. Update the above graph “Number of Confirmed Cases by US County” to 9/26/2020 and use a different color scheme or theme

  4. Make an interactive plot using a state of your chosing using a theme different from used in the above exammples.

  5. Create a report with static maps and interactive graphs that is meant to be read by others (e.g. your friends and family). Hide warnings, messages and even the code you used so that it is readable. Included references. Link to the Lab 6 report from your Github site. Submit the link to Moodle. Hide warnings, messages and even the code you used so that it is readable. Included references. Link to the Lab 6 report from your Github site. Submit the link to Moodle.